Fixed in r3387. Now menu items that do specify a keybinding will send a keyboard event directly to the TeXmacs widget (bypassing the Qt widget layer, in particular they are not converted in QKeyEvent). Maybe it would be nice if we conditionally activate the shortcut or the command depending on the mode of activation of the menu item (click->command, shortcut->keypress).

Yes, this last workaround is more or less what I proposed.
Of course, it would be better if we could distinguish whether
the event was triggered by a menu or the keyboard.
Does Qt provide some way to do this? Maybe you can ask
on some mailing list.

One shortcut which examplifies the problem is A-[ tab
(with auto-closing brackets). The A-[ shortcut produces [].
Next, pressing tab undoes the insertion of [] and inserts [[
instead (in order to create a right-open french interval).
Yet other intervals can be produced by repeatedly pressing tab.

btw: Is it possible to define a keybinding for the current window,
which overrides the binding from the menu, but yet leaves
the binding in the menu being displayed?

A possible workaround: upon activation menu items which are associated to a shortcut will not execute their command but generate a keyboard event. This keyboard event will be subsequently handled by texmacs and generate an action.
This will work under the assumption that menu items generate exaclty the same action (when clicked for example) as the associated to shortcut.
Drawback is the clicking on the menu item associated to shortcut X will be indistinguishable to typing X (so for example click+var will be interpreted as X var).

Your proposed workaround will not work properly since the same action is taken when a menu item is selecter or when the corresponding shortcut is activated. Discriminating between the two origins would lead to cumbersome code (maybe should be considerer as a last option to fix this problem).
I do not understand this issue: if TeXmacs claims that keybinding X is associated to a given command then this command should be performed whenever the binding is pressend independently of subsequent keys.

Currently, when defining a keyboard shortcut for a menu command,
Qt automatically enables this keyboard shortcut for the widget.
The corresponding keyboard events are no longer sent to TeXmacs,
and the commands are directly executed by Qt.

This is incompatible with the TeXmacs shortcut system.
For instance, assume that "X" is some shortcut,
occurring in the menus, but "X var" is also a shortcut.
Then the shortcut "X var" will never be executed,
because the key-press "X" is never sent to TeXmacs:
when pressing "X", the shortcut command is directly
executed by Qt.

A possible workaround might be to bind the Qt keyboard shortcut
to a command which simply generates the corresponding keyboard
events for TeXmacs. In the above example, the command associated
to the shortcut "X" would just send a keypress "X" event
to TeXmacs.